Simple metabolites derived from common substrates are key candidates for host-microbiota crosstalk due to the potential for convergent biosynthetic pathways. Several human signaling molecules are simple structures derived from aromatic amino acids (phenylalanine, tryptophan, and tyrosine). In this thesis, I employed targeted and untargeted mass spectrometry-based approaches to identify novel bacterial metabolites that derived from aromatic amino acids. In chapter 2, I used a 3-step mass spectrometry pipeline to identify microbiota-dependent aromatic amino acid-derived signaling molecules in vivo, identify their commensal microbial producers and identify their biosynthetic genes. This led to the identification of Enterococci and Streptococci as commensal sources of LacPhe, an exercise-inducible metabolite that regulates appetite. Monocolonization of germ-free mice with Streptococcus restored the physiological concentration of LacPhe in the ileum, and analysis of human microbiome datasets revealed the microbial LacPhe biosynthetic gene, pepV, was abundant in the GI tract and correlated inversely with obesity. This study provides an example of cross-kingdom metabolite overlap and suggests that the microbiota's impact on LacPhe metabolism should be considered when examining the effect this metabolite has on appetite and obesity. In charpter 3, I described an untargeted metabolomics approach to profile the aromatic amino acid-derived metabolome of the gut microbiota. By feeding individual bacterial species with each aromatic amino acids, I discovered that these aromatic amino acids generate a diverse metabolome, much of which is absent from the current metabolite database. Among the 80 strains of human-isolated bacteria, C. difficile produces the largest number of metabolites, primarily beloning to Nacyl amino acids. Through comparison with synthetic standards, I identified 28 novel C. difficile-specific metabolites. Furthermore, C. difficile demonstrated the highest production levels of phenylacetic acid, a precursor of negative allosteric modulator (NAM) for β2-adrenergic receptor (β2AR). This work highlights several interesting metabolites specific to C. difficile, with potential biological roles that warrant further exploration.
","abstract_html":"<p>Simple metabolites derived from common substrates are key candidates for host-microbiota crosstalk due to the potential for convergent biosynthetic pathways. Several human signaling molecules are simple structures derived from aromatic amino acids (phenylalanine, tryptophan, and tyrosine). In this thesis, I employed targeted and untargeted mass spectrometry-based approaches to identify novel bacterial metabolites that derived from aromatic amino acids. In chapter 2, I used a 3-step mass spectrometry pipeline to identify microbiota-dependent aromatic amino acid-derived signaling molecules in vivo, identify their commensal microbial producers and identify their biosynthetic genes. This led to the identification of <em>Enterococci</em> and <em>Streptococci</em> as commensal sources of LacPhe, an exercise-inducible metabolite that regulates appetite. Monocolonization of germ-free mice with <em>Streptococcus</em> restored the physiological concentration of LacPhe in the ileum, and analysis of human microbiome datasets revealed the microbial LacPhe biosynthetic gene,<em> pep</em>V, was abundant in the GI tract and correlated inversely with obesity. This study provides an example of cross-kingdom metabolite overlap and suggests that the microbiota's impact on LacPhe metabolism should be considered when examining the effect this metabolite has on appetite and obesity. In charpter 3, I described an untargeted metabolomics approach to profile the aromatic amino acid-derived metabolome of the gut microbiota. By feeding individual bacterial species with each aromatic amino acids, I discovered that these aromatic amino acids generate a diverse metabolome, much of which is absent from the current metabolite database. Among the 80 strains of human-isolated bacteria, C. <em>difficile</em> produces the largest number of metabolites, primarily beloning to Nacyl amino acids. Through comparison with synthetic standards, I identified 28 novel C. <em>difficile</em>-specific metabolites. Furthermore, C. <em>difficile</em> demonstrated the highest production levels of phenylacetic acid, a precursor of negative allosteric modulator (NAM) for β2-adrenergic receptor (β2AR). This work highlights several interesting metabolites specific to C. <em>difficile</em>, with potential biological roles that warrant further exploration.</p>","abstract_has_math":false,"creators":["Hsieh, David Chun-cheng"],"institution":null,"degree_name":"Doctor of Philosophy (PhD)","degree_level":"Thesis","degree_discipline":null,"degree_department":null,"school":null,"contributors":["Sean F. Brady"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2025,"date_issued":"2025-01-01T08:00:00Z","date_published":"2025-01-01T08:00:00Z","updated_at":"2026-07-24T04:10:47Z","subjects":["microbiota","aromatic amino acids","metabolites","mass spectrometry","LacPhe","Clostridioides difficile","Life Sciences"],"languages":[],"rights":[],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"https://digitalcommons.rockefeller.edu/student_theses_and_dissertations/807","outbound_label":"Repository record","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Sean F. Brady"]},{"key":"dc:creator","label":"Author","values":["Hsieh, David Chun-cheng"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.available","label":"Dc Date Available","values":["2027-04-15T07:00:00Z"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Thesis"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Doctor of Philosophy (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["microbiota","aromatic amino acids","metabolites","mass spectrometry","LacPhe","Clostridioides difficile","Life Sciences"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["https://digitalcommons.rockefeller.edu/student_theses_and_dissertations/807"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Simple metabolites derived from common substrates are key candidates for host-microbiota crosstalk due to the potential for convergent biosynthetic pathways. Several human signaling molecules are simple structures derived from aromatic amino acids (phenylalanine, tryptophan, and tyrosine). In this thesis, I employed targeted and untargeted mass spectrometry-based approaches to identify novel bacterial metabolites that derived from aromatic amino acids. In chapter 2, I used a 3-step mass spectrometry pipeline to identify microbiota-dependent aromatic amino acid-derived signaling molecules in vivo, identify their commensal microbial producers and identify their biosynthetic genes. This led to the identification of Enterococci and Streptococci as commensal sources of LacPhe, an exercise-inducible metabolite that regulates appetite. Monocolonization of germ-free mice with Streptococcus restored the physiological concentration of LacPhe in the ileum, and analysis of human microbiome datasets revealed the microbial LacPhe biosynthetic gene, pepV, was abundant in the GI tract and correlated inversely with obesity. This study provides an example of cross-kingdom metabolite overlap and suggests that the microbiota's impact on LacPhe metabolism should be considered when examining the effect this metabolite has on appetite and obesity. In charpter 3, I described an untargeted metabolomics approach to profile the aromatic amino acid-derived metabolome of the gut microbiota. By feeding individual bacterial species with each aromatic amino acids, I discovered that these aromatic amino acids generate a diverse metabolome, much of which is absent from the current metabolite database. Among the 80 strains of human-isolated bacteria, C. difficile produces the largest number of metabolites, primarily beloning to Nacyl amino acids. Through comparison with synthetic standards, I identified 28 novel C. difficile-specific metabolites. Furthermore, C. difficile demonstrated the highest production levels of phenylacetic acid, a precursor of negative allosteric modulator (NAM) for β2-adrenergic receptor (β2AR). This work highlights several interesting metabolites specific to C. difficile, with potential biological roles that warrant further exploration.
"]},{"key":"dc:title","label":"Title","values":["Aromatic Amino Acid Metabolome In The Human Gut Microbiota"]}]}],"canonical_facts":{"dc:contributor":["Sean F. Brady"],"dc:creator":["Hsieh, David Chun-cheng"],"dc:date.available":["2027-04-15T07:00:00Z"],"dc:description.abstract":["Simple metabolites derived from common substrates are key candidates for host-microbiota crosstalk due to the potential for convergent biosynthetic pathways. Several human signaling molecules are simple structures derived from aromatic amino acids (phenylalanine, tryptophan, and tyrosine). In this thesis, I employed targeted and untargeted mass spectrometry-based approaches to identify novel bacterial metabolites that derived from aromatic amino acids. In chapter 2, I used a 3-step mass spectrometry pipeline to identify microbiota-dependent aromatic amino acid-derived signaling molecules in vivo, identify their commensal microbial producers and identify their biosynthetic genes. This led to the identification of Enterococci and Streptococci as commensal sources of LacPhe, an exercise-inducible metabolite that regulates appetite. Monocolonization of germ-free mice with Streptococcus restored the physiological concentration of LacPhe in the ileum, and analysis of human microbiome datasets revealed the microbial LacPhe biosynthetic gene, pepV, was abundant in the GI tract and correlated inversely with obesity. This study provides an example of cross-kingdom metabolite overlap and suggests that the microbiota's impact on LacPhe metabolism should be considered when examining the effect this metabolite has on appetite and obesity. In charpter 3, I described an untargeted metabolomics approach to profile the aromatic amino acid-derived metabolome of the gut microbiota. By feeding individual bacterial species with each aromatic amino acids, I discovered that these aromatic amino acids generate a diverse metabolome, much of which is absent from the current metabolite database. Among the 80 strains of human-isolated bacteria, C. difficile produces the largest number of metabolites, primarily beloning to Nacyl amino acids. Through comparison with synthetic standards, I identified 28 novel C. difficile-specific metabolites. Furthermore, C. difficile demonstrated the highest production levels of phenylacetic acid, a precursor of negative allosteric modulator (NAM) for β2-adrenergic receptor (β2AR). This work highlights several interesting metabolites specific to C. difficile, with potential biological roles that warrant further exploration.
"],"dc:identifier":["https://digitalcommons.rockefeller.edu/student_theses_and_dissertations/807"],"dc:subject":["microbiota","aromatic amino acids","metabolites","mass spectrometry","LacPhe","Clostridioides difficile","Life Sciences"],"dc:title":["Aromatic Amino Acid Metabolome In The Human Gut Microbiota"],"thesis:degree_level":["Thesis"],"thesis:degree_name":["Doctor of Philosophy (PhD)"]},"updated_at":"2026-07-24T04:10:47Z"}